ArticleSoil biology & biochemistry2012
Soil metaproteomics - Comparative evaluation of protein extraction protocols.
Article in Soil biology & biochemistry, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 51 papers, 1 of them a synthesis that pooled it.
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Who cites it
51 citing papers in PubMed, 1 synthesis or guideline pooled it.
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- Functional Express Proteomics for Search and Identification of Differentially Regulated Proteins Involved in the Reaction of Wheat (International journal of molecular sciences · 2025Article
- The microbiologist's guide to metaproteomics.iMeta · 2025Review
- Systematic evaluation of protein extraction for metaproteomic analysis of marine sediment with high clay content.ISME communications · 2025Article
- Soil Metaproteomics for Microbial Community Profiling: Methodologies and Challenges.Current microbiology · 2024Review
- Extraction of Proteins from Fermented Food.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Extraction of active, contaminant degrading enzymes from soil.Applied soil ecology : a section of Agriculture, Ecosystems & Environment · 2023Article
- A Simple Biochemical Method for the Detection of Proteins as Biomarkers of Life on Martian Soil Simulants and the Impact of UV Radiation.Life (Basel, Switzerland) · 2023Article
- Metaproteomics to understand how microbiota function: The crystal ball predicts a promising future.Environmental microbiology · 2023Article
- Micro-scale Experimental System Coupled with Fluorescence-based Estimation of Fungal Biomass to Study Utilisation of Plant Substrates.Microbial ecology · 2022Article
- Evaluation of RNAMicrobiology spectrum · 2021Article
- Increasing the power of interpretation for soil metaproteomics data.Microbiome · 2021Article
- Revealing taxon-specific heavy metal-resistance mechanisms in denitrifying phosphorus removal sludge using genome-centric metaproteomics.Microbiome · 2021Article
- Rainforest-to-pasture conversion stimulates soil methanogenesis across the Brazilian Amazon.The ISME journal · 2021Article
Corrections and comments
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Authors and funding
8 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Metaproteomics and its potential applications are very promising to study microbial activity in environmental samples and to obtain a deeper understanding of microbial interactions. However, due to the complexity of soil samples the exhaustive extraction of proteins is a major challenge. We compared soil protein extraction protocols in terms of their protein extraction efficiency for two different soil types. Four different protein extraction procedures were applied based on (a) SDS extraction without phenol, (b) NaOH and subsequent phenol extraction, (c) SDS-phenol extraction and (d) SDS-phenol extraction with prior washing steps. To assess the suitability of these methods for the functional analysis of the soil metaproteome, they were applied to a potting soil high in organic matter and a forest soil. Proteins were analyzed by two-dimensional liquid chromatography/tandem mass spectrometry (2D-LC-MS/MS) and the number of unique spectra as well as the number of assigned proteins for each of the respective protocols was compared. In both soil types, extraction with SDS-phenol (c) resulted in "high" numbers of proteins. Moreover, a spiking experiment was conducted to evaluate protein recovery. To this end sterilized forest soil was amended with proteins from pure cultures of Pectobacterium carotovorum and Aspergillus nidulans. The protein recovery in the spiking experiment was almost 50%. Our study demonstrates that a critical evaluation of the extraction protocol is crucial for the quality of the metaproteomics data, especially in highly complex samples like natural soils.
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Registered trials
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